Ok so I have a FTP server running on Windows 2003. Well I want to make a folder where my users can drop files in. But that is the only folder that I want them to be able to drop files in.

In IIS if i give the FTP site write access it will let me drop what I want where I want. If I take away the write access but give my users write access to that folder it wont let them write to the upload folder. Anyone have any ideas how to make it so only one folder in my FTP site has write access?

Don't explicitly deny write access-- just don't set it. Then, set explicit write permissions on the folder you choose. That should do it-- when applying permissions in Windows, the most restrictive permissions always take precedence over others.